Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies
Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies
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DOI：
10.1093/oxfordjournals.molbev.a025664
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发表时间：
1996-09-01
影响因子：
10.7
通讯作者：
vonHaeseler, A
中科院分区：
文献类型：
--
作者：
Strimmer, K;vonHaeseler, A
引入了一种通用方法“四重拼图”，根据 DNA 或氨基酸序列数据重建系统发育树的拓扑（分支模式）。该方法将最大似然树重建应用于可以由 n 个序列形成的所有可能的四重奏。四重树作为重建一组最佳 n 分类树的起点。这些树的多数规则共识定义了四重令人费解的树，并显示了得到良好支持的分组。计算机模拟表明，四重拼图重建真实树的性能始终等于或优于邻居连接。对于某些具有高转换/颠换偏差的情况，四重组谜题的性能比邻接连接高出 10 倍。四重组谜题对羊膜动物线粒体 RNA 和 tRNA(Val) 序列的应用证明了该方法的强大功能。可以使用与 PHYLIP 兼容的 ANSI C 程序 PUZZLE，用于分析核苷酸或氨基酸序列数据。
A versatile method, quartet puzzling, is introduced to reconstruct the topology (branching pattern) of a phylogenetic tree based on DNA or amino acid sequence data. This method applies maximum-likelihood tree reconstruction to all possible quartets that can be formed from n sequences. The quartet trees serve as starting points to reconstruct a set of optimal n-taxon trees. The majority rule consensus of these trees defines the quartet puzzling tree and shows groupings that are well supported. Computer simulations show that the performance of quartet puzzling to reconstruct the true tree is always equal to or better than that of neighbor joining. For some cases with high transition/transversion bias quartet puzzling outperforms neighbor joining by a factor of 10. The application of quartet puzzling to mitochondrial RNA and tRNA(Val) sequences from amniotes demonstrates the power of the approach. A PHYLIP-compatible ANSI C program, PUZZLE, for analyzing nucleotide or amino acid sequence data is available.